Metadata-Version: 2.1
Name: scingestor
Version: 0.0.3
Summary: Scientific Catalog Tools
Home-page: http://github.com/jkotan/scingestor
Author: ('Jan Kotanski',)
Author-email: jankotan@gmail.com
Maintainer: Jan Kotanski
Maintainer-email: jankotan@gmail.com
License: GNU GENERAL PUBLIC LICENSE, version 3
Description: # Scicat Dataset Ingestor
        
        ![github workflow](https://github.com/jkotan/scingestor/actions/workflows/tests.yml/badge.svg) [![docs](https://img.shields.io/badge/Documentation-webpages-ADD8E6.svg)](https://jkotan.github.io/scingestor/index.html) [![Pypi Version](https://img.shields.io/pypi/v/scingestor.svg)](https://pypi.python.org/pypi/scingestor) [![Python Versions](https://img.shields.io/pypi/pyversions/scingestor.svg)](https://pypi.python.org/pypi/scingestor/)
        
        The `scingestor` python package provides a support for scripts which ingest RawDatasets and OrigDatablocks into the SciCat metadata server.
        
        ## scicat_dataset_ingestor
        SciCat Dataset ingestor server ingests scan metadata just after a scan is finished. It can be executed by
        
        ```
        scicat_dataset_ingestor -c ~/.scingestor.yaml
        ```
        Its configuration written in YAML can contain the following variables
        * `scicat_url` (str)
        * `ingestor_credential_file` (str)
        * `beamtime_dirs` (list\<str\>)  or  `beamtime_base_dir` (str)
        * `ingestor_log_dir` (str)
        * `ingestor_username` (str)
        * `doi_prefix` (str)
        * `update_strategy` (`patch`, `create`, `mixed`)
        * `relative_path_in_datablock` (bool)
        * `chmod_json_files` (str)
        * `oned_in_metadata` (bool)
        * `scan_metadata_postfix` (str)
        * `datablock_metadata_postfix` (str)
        * `beamtime_filename_postfix` (str)
        * `beamtime_filename_prefix` (str)
        * `datasets_filename_pattern` (str)
        * `ingested_datasets_filename_pattern` (str)
        * `nxs_dataset_metadata_generator` (str)
        * `dataset_metadata_generator` (str)
        * `datablock_metadata_generator` (str)
        * `datablock_metadata_stream_generator` (str)
        * `datablock_metadata_generator_scanpath_postfix` (str)
        * `inotify_timeout` (float)
        * `get_event_timeout` (float)
        * `ingestion_delay_time` (float)
        * `max_request_tries_number` (int)
        * `request_headers` (dict\<str,str\>)
        * `scicat_datasets_path` (str)
        * `scicat_datablocks_path` (str)
        * `scicat_users_login_path` (str)
        * `metadata_keywords_without_checks` (list\<str\>)
        
        e.g.
        ```
        beamtime_dirs:
          - /home/jkotan/gpfs/current
          - /home/jkotan/gpfs/commissioning
        scicat_url: http://localhost:8881
        ingestor_credential_file: /home/jkotan/gpfs/pwd
        ```
        
        ## scicat_dataset_ingest
        
        Re-ingestion script for SciCat RawDatasets and OrigDatablocks is usually performed at the end of the beamtime.
        ```
        scicat_dataset_ingest -c ~/.scingestor.yaml
        ```
        Its configuration written YAML like for `scicat_dataset_ingestor`
        ## Installation
        
        ### Required packages
        
        * python3 >= 3.7
        * nxstools >= 3.28.0
        * inotifyx (python3 version)
        * requests
        * setuptools
        * pyyaml
        * pytest (to run tests)
        * sphinx (to build the documentation)
        
        
        ### Install from sources
        
        The code from https://github.com/jkotan/scingestor can be built with
        
        ```
        python3 setup.py install
        ```
        
        
        To build the documentation use
        
        ```
        python3 setup.py build_sphinx
        ```
        
        The resulting documentation can be found below `build/sphinx/html` in the root
        directory of the source distribution.
        
        Finally, the package can be tested using
        
        ```
        python3 -m pytest test
        ```
        
        ### Install in conda or pip environment
        
        The code can be installed in your conda environment by
        ```
        conda create -n myenv python=3.9
        conda activate myenv
        
        pip install inotifyx-py3
        pip install scingestor
        ```
        
        or in your pip environment by
        ```
        python3 -m venv myvenv
        . myvenv/bin/activate
        
        pip install inotifyx-py3
        pip install scingestor
        ```
        
        
        ### Debian and Ubuntu packages
        
        Debian  `bullseye`, `buster`  or Ubuntu  `jammy`, `focal` packages can be found in the HDRI repository.
        
        To install the debian packages, add the PGP repository key
        
        ```
        sudo su
        curl -s http://repos.pni-hdri.de/debian_repo.pub.gpg  | gpg --no-default-keyring --keyring gnupg-ring:/etc/apt/trusted.gpg.d/debian-hdri-repo.gpg --import
        chmod 644 /etc/apt/trusted.gpg.d/debian-hdri-repo.gpg
        ```
        
        and then download the corresponding source list, e.g.
        for `bullseye`
        
        ```
        cd /etc/apt/sources.list.d
        wget http://repos.pni-hdri.de/bullseye-pni-hdri.list
        ```
        
        or `jammy`
        
        ```
        cd /etc/apt/sources.list.d
        wget http://repos.pni-hdri.de/jammy-pni-hdri.list
        ```
        respectively.
        
        Finally,
        
        ```
        apt-get update
        apt-get install python3-scingestor
        ```
        
Keywords: metadata catalog tools metadata photon science
Platform: Linux
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Description-Content-Type: text/markdown
